Lattice Light-Sheet | Organoids | ML and Big Data | Optical Tweezing | Reaction-Diffusion | Fun


Enjoy browsing my science!

4D Lattice Light-Sheet Organoid Imaging

I use endogenously GFP/RFP tagged stem cells to grow tissues (organoids) and then image them live with the lattice light-sheet microscope (LLSM). Shown below is a young brain organoid and a polarized intestinal organoid. LLSM imaging is done at superresolution with seconds frame rates. The resulting large datasets (terabytes) are analyzed using my custom analysis software pyLattice.

J Schöneberg, D Dambournet, T-L Liu, R Forster, D Hockemeyer, E Betzig, D G Drubin (2018) 4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell derived intestinal organoids. Molecular Biology of the Cell, 29(24).

pyLattice - Machine Learning-based Lattice Light-Sheet Data Analytics

pyLattice is a python library for advanced lattice light-sheet image analysis. Collaborate with us on gitHub and read about how we solve big data analytics challenges when we analyze big LLSM datasets.

J Schöneberg, G Raghupathi, E Betzig, D G Drubin (2019) 3D Deep Convolutional Neural Networks in Lattice Light-Sheet Data Puncta Segmentation. IEEE Proceedings International Conference on Bioinformatics and Biomedicine (BIBM), in press.

Scope Engineering and Optical Tweezing

I combined confocal microscopy with optical trapping to measure force and fluorescence of proteins acting on small membrane nanotubes (pulled from e.g. a giant unilamellar vesicles (GUV)). These nanotubes allow studying protein-membrane biophysics in tubular, highly curved topologies. They resemble vesicle necks found e.g. in normal topology budding (e.g. Clathrin mediated endocytosis) and reverse topology budding (ESCRT system).

The Confleezers: Left:The Confleezers 1.0 that combines confocal microscopy with optical tweezing. Right: Membrane nanotubes pulled from model membranes using micromanipulators (top) and the trap of the Confleezers (bottom).

See our applications on the ESCRT system and our review:

J Schöneberg, M R Pavlin*, S Yan*, M Righini, I-H Lee, L-A Carlson, A H Bahrami, D H Goldman, X Ren, G Hummer, C Bustamante and J H Hurley (2018) ATP-dependent force generation and membrane scission by ESCRT-III and Vps4, Science, 362 (6421), 1423-1428. * equal contribution.

J Schöneberg*, Lee IH*, Iwasa JH, Hurley JH, (2016) Reverse-topology membrane scission by the ESCRT proteins. Nature Reviews Molecular Cell Biology, doi: 10.1038/nrm.2016.12. (*equal contribution).


J Schöneberg*, M Lehmann*, A Ullrich, Y Posor, W-T Lo, G Lichtner, J Schmoranzer, V Haucke, F Noé, (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nature Communications 8, 15873 doi: 10.1038/ncomms15873. (*equal contribution).


ReaDDy is a particle-based reaction-diffusion simulation software. It features

  1. simulation in and on arbitrary geometries (i.e. 3D, 2D, spherical,...),

  2. spatial confinement (walls, boxes, tubes, ...),

  3. excluded volume of particles (crowding effects) and

  4. particle-particle interaction potentials (repulsion, attraction, clustering, ...).

See more under, contribute under gitHub/readdy and read the paper under Schöneberg and Noé, PLOS ONE, 2013. Also check out the newest ReaDDy developments here.


In MCB at UC Berkeley, I currently work in the Drubin, Hockemeyer and Betzig labs. I have worked in the Hurley, Bustamante and Hummer labs. Download pyLattice and ReaDDy and collaborate with us on gitHub.